Starting phenix.real_space_refine
on Fri Aug 22 17:57:19 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8urt_42500/08_2025/8urt_42500.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      4      5.21       5
     S      42      5.16       5
     C    4474      2.51       5
     N     956      2.21       5
     O    1140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6622
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
    Chain: "B"
      Number of atoms: 3120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
    Chain: "A"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 244
          Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 4}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 136
          Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.56, per 1000 atoms: 0.24
  Number of scatterers: 6622
  At special positions: 0
  Unit cell: (89.64, 103.68, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       6     15.00
     Mg      4     11.99
     O    1140      8.00
     N     956      7.00
     C    4474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 345.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      79.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 14
      removed outlier: 4.757A  pdb=" N   GLY A  11 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LYS A  14 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 30 through 39
      removed outlier: 4.302A  pdb=" N   PHE A  34 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 70
      removed outlier: 4.099A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ILE A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 3.721A  pdb=" N   PHE A  83 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A  86 " --> pdb=" O   TYR A  82 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ARG A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A 105 " --> pdb=" O   MET A 101 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 106 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 137
      removed outlier: 3.713A  pdb=" N   GLU A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   THR A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 141 through 165
      removed outlier: 3.905A  pdb=" N   ILE A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   SER A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 3.793A  pdb=" N   ILE A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 200
    Processing helix  chain 'A' and resid 217 through 250
    Processing helix  chain 'A' and resid 256 through 267
    Processing helix  chain 'A' and resid 268 through 285
      removed outlier: 3.649A  pdb=" N   PHE A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 289
      removed outlier: 3.904A  pdb=" N   ILE A 289 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 286 through 289'
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 322 through 325
    Processing helix  chain 'A' and resid 326 through 341
    Processing helix  chain 'A' and resid 349 through 381
      removed outlier: 4.284A  pdb=" N   TRP A 355 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 15
      removed outlier: 4.753A  pdb=" N   GLY B  11 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B  14 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 30 through 39
      removed outlier: 4.403A  pdb=" N   PHE B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'B' and resid 50 through 70
    Processing helix  chain 'B' and resid 78 through 107
      removed outlier: 3.972A  pdb=" N   TYR B  82 " --> pdb=" O   PRO B  78 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLY B 100 " --> pdb=" O   ASP B  96 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   MET B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 137
      removed outlier: 3.704A  pdb=" N   GLU B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
    Processing helix  chain 'B' and resid 141 through 166
      removed outlier: 3.870A  pdb=" N   ILE B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 193
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 217 through 252
      removed outlier: 4.142A  pdb=" N   ASN B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B 250 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   SER B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 266
      removed outlier: 3.504A  pdb=" N   THR B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 285
    Processing helix  chain 'B' and resid 286 through 289
      removed outlier: 3.984A  pdb=" N   ILE B 289 " --> pdb=" O   PRO B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 289'
    Processing helix  chain 'B' and resid 290 through 315
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 341
      removed outlier: 3.587A  pdb=" N   LEU B 332 " --> pdb=" O   PRO B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 381
      removed outlier: 3.833A  pdb=" N   ILE B 349 " --> pdb=" O   GLN B 345 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL B 350 " --> pdb=" O   LYS B 346 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   SER B 351 " --> pdb=" O   GLY B 347 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 348 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204
      removed outlier: 7.146A  pdb=" N   VAL A 215 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 205
      removed outlier: 7.370A  pdb=" N   VAL B 215 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 932
        1.31 -     1.43: 2069
        1.43 -     1.56: 3727
        1.56 -     1.68: 22
        1.68 -     1.81: 68
  Bond restraints: 6818
  Sorted by residual:
  bond pdb=" C11 PCW A1003 "
       pdb=" O3  PCW A1003 "
    ideal  model  delta    sigma   weight residual
    1.326  1.421 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C11 PCW A1004 "
       pdb=" O3  PCW A1004 "
    ideal  model  delta    sigma   weight residual
    1.326  1.421 -0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" C11 PCW A1006 "
       pdb=" O3  PCW A1006 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" C11 PCW B 401 "
       pdb=" O3  PCW B 401 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.19e+01
  bond pdb=" C11 PCW A1007 "
       pdb=" O3  PCW A1007 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.19e+01
  ... (remaining 6813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 9144
        5.03 -    10.07: 58
       10.07 -    15.10: 15
       15.10 -    20.14: 9
       20.14 -    25.17: 12
  Bond angle restraints: 9238
  Sorted by residual:
  angle pdb=" C19 PCW A1007 "
        pdb=" C20 PCW A1007 "
        pdb=" C21 PCW A1007 "
      ideal   model   delta    sigma   weight residual
     127.82  152.99  -25.17 3.00e+00 1.11e-01 7.04e+01
  angle pdb=" C19 PCW B 404 "
        pdb=" C20 PCW B 404 "
        pdb=" C21 PCW B 404 "
      ideal   model   delta    sigma   weight residual
     127.82  152.99  -25.17 3.00e+00 1.11e-01 7.04e+01
  angle pdb=" C19 PCW B 401 "
        pdb=" C20 PCW B 401 "
        pdb=" C21 PCW B 401 "
      ideal   model   delta    sigma   weight residual
     127.82  152.75  -24.93 3.00e+00 1.11e-01 6.91e+01
  angle pdb=" C19 PCW A1004 "
        pdb=" C20 PCW A1004 "
        pdb=" C21 PCW A1004 "
      ideal   model   delta    sigma   weight residual
     127.82  152.71  -24.89 3.00e+00 1.11e-01 6.89e+01
  angle pdb=" C19 PCW A1006 "
        pdb=" C20 PCW A1006 "
        pdb=" C21 PCW A1006 "
      ideal   model   delta    sigma   weight residual
     127.82  152.58  -24.76 3.00e+00 1.11e-01 6.81e+01
  ... (remaining 9233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.25: 3634
       31.25 -    62.50: 279
       62.50 -    93.75: 34
       93.75 -   125.00: 2
      125.00 -   156.25: 5
  Dihedral angle restraints: 3954
    sinusoidal: 1676
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" N   PCW A1003 "
           pdb=" C4  PCW A1003 "
           pdb=" C5  PCW A1003 "
           pdb=" O4P PCW A1003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  137.09  156.25     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" N   PCW B 404 "
           pdb=" C4  PCW B 404 "
           pdb=" C5  PCW B 404 "
           pdb=" O4P PCW B 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  148.19  145.15     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" N   PCW B 401 "
           pdb=" C4  PCW B 401 "
           pdb=" C5  PCW B 401 "
           pdb=" O4P PCW B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  158.33  135.01     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 755
       0.044 -    0.088: 199
       0.088 -    0.133: 38
       0.133 -    0.177: 0
       0.177 -    0.221: 6
  Chirality restraints: 998
  Sorted by residual:
  chirality pdb=" C2  PCW A1003 "
            pdb=" C1  PCW A1003 "
            pdb=" C3  PCW A1003 "
            pdb=" O2  PCW A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" C2  PCW B 404 "
            pdb=" C1  PCW B 404 "
            pdb=" C3  PCW B 404 "
            pdb=" O2  PCW B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" C2  PCW A1006 "
            pdb=" C1  PCW A1006 "
            pdb=" C3  PCW A1006 "
            pdb=" O2  PCW A1006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 995 not shown)

  Planarity restraints: 1102
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  47 "   -0.037 5.00e-02 4.00e+02   5.72e-02 5.23e+00
        pdb=" N   PRO A  48 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 160 "    0.012 2.00e-02 2.50e+03   8.36e-03 1.75e+00
        pdb=" CG  TRP B 160 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 160 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 160 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 160 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 160 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 160 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 169 "    0.008 2.00e-02 2.50e+03   8.93e-03 1.60e+00
        pdb=" CG  TYR A 169 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 169 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 169 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 169 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 169 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 169 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 169 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1099 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 35
        2.58 -     3.16: 5157
        3.16 -     3.74: 9936
        3.74 -     4.32: 13508
        4.32 -     4.90: 23579
  Nonbonded interactions: 52215
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  92 "
            pdb="MG    MG B 403 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MG    MG A1001 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" OD2 ASP B 117 "
            pdb="MG    MG B 402 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" OD2 ASP A  96 "
            pdb="MG    MG A1002 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O   PRO B  78 "
            pdb=" OG1 THR B  81 "
     model   vdw
     2.138 3.040
  ... (remaining 52210 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 388 or resid 1002 or resid 1004 through 1005))
  selection = (chain 'B' and (resid 1 through 388 or resid 402 or resid 404 through 405))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.260
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.095   6818  Z= 0.406
  Angle     :  1.441  25.171   9238  Z= 0.529
  Chirality :  0.041   0.221    998
  Planarity :  0.004   0.057   1102
  Dihedral  : 21.441 156.245   2494
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.59 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.31), residues: 770
  helix:  2.48 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.022   0.001   TYR A 169 
 PHE   0.014   0.001   PHE B 206 
 TRP   0.023   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00811 ( 6818)
  covalent geometry    : angle       1.44070 ( 9238)
  hydrogen bonds       : bond        0.13049 (  442)
  hydrogen bonds       : angle       4.74858 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  128 SER cc_start: 0.8486 (t) cc_final: 0.8104 (p)
REVERT: A  326 LEU cc_start: 0.7443 (mt) cc_final: 0.7204 (mt)
REVERT: B   41 ILE cc_start: 0.7719 (tt) cc_final: 0.7284 (mm)
REVERT: B  127 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6346 (mp)
REVERT: B  128 SER cc_start: 0.8467 (t) cc_final: 0.8047 (p)
REVERT: B  168 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6178 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0555
  time to fit residues: 6.9035
Evaluate side-chains
  80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  290 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.135239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.097629 restraints weight = 68223.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.099477 restraints weight = 47342.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.098397 restraints weight = 37653.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.098509 restraints weight = 39686.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.098485 restraints weight = 36230.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.0628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6818  Z= 0.120
  Angle     :  0.503   6.355   9238  Z= 0.245
  Chirality :  0.038   0.120    998
  Planarity :  0.004   0.054   1102
  Dihedral  : 20.170 137.674   1145
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.98 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.31), residues: 770
  helix:  2.67 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.33 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.011   0.001   TYR B 274 
 PHE   0.012   0.001   PHE B 206 
 TRP   0.017   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6818)
  covalent geometry    : angle       0.50275 ( 9238)
  hydrogen bonds       : bond        0.04877 (  442)
  hydrogen bonds       : angle       3.90136 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   99 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6910 (p0)
REVERT: A  193 TYR cc_start: 0.8705 (m-80) cc_final: 0.8437 (m-80)
REVERT: B    7 GLN cc_start: 0.7125 (tp40) cc_final: 0.6587 (pt0)
REVERT: B   41 ILE cc_start: 0.8172 (tt) cc_final: 0.7621 (mm)
REVERT: B  388 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.4792 (tptt)
  outliers start: 16
  outliers final: 11
  residues processed: 84
  average time/residue: 0.0510
  time to fit residues: 6.5235
Evaluate side-chains
  77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.141542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.099429 restraints weight = 66291.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.100366 restraints weight = 39772.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.100924 restraints weight = 36485.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.101000 restraints weight = 35018.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.100988 restraints weight = 31897.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6818  Z= 0.124
  Angle     :  0.494   6.039   9238  Z= 0.241
  Chirality :  0.038   0.119    998
  Planarity :  0.004   0.050   1102
  Dihedral  : 18.278 133.524   1136
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.25 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.31), residues: 770
  helix:  2.74 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.31 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 307 
 TYR   0.016   0.001   TYR A 169 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6818)
  covalent geometry    : angle       0.49378 ( 9238)
  hydrogen bonds       : bond        0.04852 (  442)
  hydrogen bonds       : angle       3.84370 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   99 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6751 (p0)
REVERT: A  193 TYR cc_start: 0.8706 (m-80) cc_final: 0.8486 (m-80)
REVERT: B    7 GLN cc_start: 0.7140 (tp40) cc_final: 0.6558 (pt0)
REVERT: B   41 ILE cc_start: 0.7969 (tt) cc_final: 0.7463 (mm)
REVERT: B  157 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: B  168 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6962 (mp)
REVERT: B  388 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.4477 (tptt)
  outliers start: 20
  outliers final: 13
  residues processed: 84
  average time/residue: 0.0511
  time to fit residues: 6.4241
Evaluate side-chains
  84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.133952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.094541 restraints weight = 68595.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.095546 restraints weight = 46178.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.095840 restraints weight = 41694.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.096000 restraints weight = 38926.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.095970 restraints weight = 36411.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6818  Z= 0.132
  Angle     :  0.501   6.107   9238  Z= 0.245
  Chirality :  0.039   0.118    998
  Planarity :  0.004   0.048   1102
  Dihedral  : 16.811 127.026   1135
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.40 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.31), residues: 770
  helix:  2.73 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.28 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 307 
 TYR   0.014   0.001   TYR A 169 
 PHE   0.013   0.001   PHE A 275 
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6818)
  covalent geometry    : angle       0.50095 ( 9238)
  hydrogen bonds       : bond        0.05066 (  442)
  hydrogen bonds       : angle       3.86802 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   99 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6808 (p0)
REVERT: A  193 TYR cc_start: 0.8694 (m-80) cc_final: 0.8477 (m-80)
REVERT: B    7 GLN cc_start: 0.7188 (tp40) cc_final: 0.6601 (pt0)
REVERT: B   41 ILE cc_start: 0.8050 (tt) cc_final: 0.7522 (mm)
REVERT: B  104 ARG cc_start: 0.6493 (mmt90) cc_final: 0.6156 (ttm110)
REVERT: B  388 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5029 (ttpp)
  outliers start: 19
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0811
  time to fit residues: 9.8297
Evaluate side-chains
  83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0670
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.140150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.098127 restraints weight = 65524.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.099444 restraints weight = 40336.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.100118 restraints weight = 32294.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.100044 restraints weight = 28466.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.100127 restraints weight = 29670.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6818  Z= 0.136
  Angle     :  0.509   6.076   9238  Z= 0.249
  Chirality :  0.039   0.139    998
  Planarity :  0.004   0.046   1102
  Dihedral  : 15.530 121.761   1135
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.11 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.31), residues: 770
  helix:  2.68 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.28 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  79 
 TYR   0.014   0.001   TYR A 169 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6818)
  covalent geometry    : angle       0.50861 ( 9238)
  hydrogen bonds       : bond        0.05175 (  442)
  hydrogen bonds       : angle       3.86400 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7370 (mtt180)
REVERT: A   99 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6735 (p0)
REVERT: A  109 GLN cc_start: 0.7324 (mt0) cc_final: 0.6772 (mp10)
REVERT: A  193 TYR cc_start: 0.8745 (m-80) cc_final: 0.8528 (m-80)
REVERT: B    7 GLN cc_start: 0.7220 (tp40) cc_final: 0.6676 (pt0)
REVERT: B   41 ILE cc_start: 0.8028 (tt) cc_final: 0.7503 (mm)
REVERT: B  104 ARG cc_start: 0.6474 (mmt90) cc_final: 0.6062 (mtm110)
REVERT: B  383 TYR cc_start: 0.8195 (m-80) cc_final: 0.7875 (m-80)
REVERT: B  388 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.4771 (ttpp)
  outliers start: 19
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0689
  time to fit residues: 8.2973
Evaluate side-chains
  82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.139662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.097814 restraints weight = 66204.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.099762 restraints weight = 40177.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.099398 restraints weight = 34261.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.099581 restraints weight = 33460.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.099359 restraints weight = 32256.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6818  Z= 0.141
  Angle     :  0.514   7.182   9238  Z= 0.251
  Chirality :  0.039   0.143    998
  Planarity :  0.004   0.045   1102
  Dihedral  : 14.889 116.985   1135
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.96 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.31), residues: 770
  helix:  2.69 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.30 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 307 
 TYR   0.014   0.001   TYR B 274 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6818)
  covalent geometry    : angle       0.51418 ( 9238)
  hydrogen bonds       : bond        0.05288 (  442)
  hydrogen bonds       : angle       3.86756 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7331 (tp40) cc_final: 0.6540 (tp40)
REVERT: A   79 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7432 (mtt180)
REVERT: A   99 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6759 (p0)
REVERT: A  109 GLN cc_start: 0.7455 (mt0) cc_final: 0.6930 (mp10)
REVERT: A  349 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (mm)
REVERT: B    7 GLN cc_start: 0.7219 (tp40) cc_final: 0.6499 (pt0)
REVERT: B   41 ILE cc_start: 0.8025 (tt) cc_final: 0.7496 (mm)
REVERT: B  104 ARG cc_start: 0.6461 (mmt90) cc_final: 0.6030 (mtm110)
REVERT: B  383 TYR cc_start: 0.8154 (m-80) cc_final: 0.7843 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0678
  time to fit residues: 8.4419
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0670
   chunk 70 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.140983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.099333 restraints weight = 66588.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.100935 restraints weight = 41278.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.101931 restraints weight = 34886.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.101764 restraints weight = 30662.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.101621 restraints weight = 28879.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6818  Z= 0.125
  Angle     :  0.499   6.256   9238  Z= 0.242
  Chirality :  0.039   0.136    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 14.353 113.146   1135
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.69 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.31), residues: 770
  helix:  2.75 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.013   0.001   TYR A 169 
 PHE   0.011   0.001   PHE A 275 
 TRP   0.014   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6818)
  covalent geometry    : angle       0.49901 ( 9238)
  hydrogen bonds       : bond        0.04884 (  442)
  hydrogen bonds       : angle       3.83334 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7092 (tp40) cc_final: 0.6372 (tp40)
REVERT: A   79 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7343 (mtt180)
REVERT: A   99 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6926 (p0)
REVERT: A  109 GLN cc_start: 0.7366 (mt0) cc_final: 0.6879 (mp10)
REVERT: A  151 ILE cc_start: 0.8229 (mt) cc_final: 0.8022 (mm)
REVERT: A  349 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8408 (mm)
REVERT: B    7 GLN cc_start: 0.7159 (tp40) cc_final: 0.6459 (pt0)
REVERT: B   41 ILE cc_start: 0.7986 (tt) cc_final: 0.7462 (mm)
REVERT: B  104 ARG cc_start: 0.6229 (mmt90) cc_final: 0.5809 (mtm110)
REVERT: B  383 TYR cc_start: 0.8108 (m-80) cc_final: 0.7766 (m-80)
REVERT: B  388 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.4759 (ttpp)
  outliers start: 17
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0693
  time to fit residues: 8.3383
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.133473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.095093 restraints weight = 68569.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.097065 restraints weight = 46011.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.096035 restraints weight = 37338.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.096030 restraints weight = 37763.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.096079 restraints weight = 36884.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6818  Z= 0.145
  Angle     :  0.520   6.787   9238  Z= 0.254
  Chirality :  0.040   0.130    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 14.139 109.386   1135
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.25 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.31), residues: 770
  helix:  2.67 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.28 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 307 
 TYR   0.014   0.001   TYR B 274 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.014   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6818)
  covalent geometry    : angle       0.52022 ( 9238)
  hydrogen bonds       : bond        0.05352 (  442)
  hydrogen bonds       : angle       3.88067 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7185 (tp40) cc_final: 0.6492 (tp40)
REVERT: A   79 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7470 (mtt180)
REVERT: A   99 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6973 (p0)
REVERT: A  109 GLN cc_start: 0.7444 (mt0) cc_final: 0.6982 (mp10)
REVERT: A  349 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8549 (mm)
REVERT: B    7 GLN cc_start: 0.7140 (tp40) cc_final: 0.6411 (pt0)
REVERT: B   41 ILE cc_start: 0.8034 (tt) cc_final: 0.7501 (mm)
REVERT: B  104 ARG cc_start: 0.6312 (mmt90) cc_final: 0.5846 (mtm110)
REVERT: B  383 TYR cc_start: 0.8136 (m-80) cc_final: 0.7765 (m-80)
REVERT: B  388 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.4763 (ttpp)
  outliers start: 21
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0703
  time to fit residues: 8.7106
Evaluate side-chains
  84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.140932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.098841 restraints weight = 65290.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.100023 restraints weight = 40717.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.101381 restraints weight = 34981.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.100799 restraints weight = 31764.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.101028 restraints weight = 29991.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6818  Z= 0.129
  Angle     :  0.506   6.604   9238  Z= 0.247
  Chirality :  0.039   0.138    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 13.755 105.672   1135
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.40 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.31), residues: 770
  helix:  2.75 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 307 
 TYR   0.012   0.001   TYR A 169 
 PHE   0.011   0.001   PHE A 275 
 TRP   0.013   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6818)
  covalent geometry    : angle       0.50614 ( 9238)
  hydrogen bonds       : bond        0.04973 (  442)
  hydrogen bonds       : angle       3.83650 ( 1293)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7143 (tp40) cc_final: 0.6419 (tp40)
REVERT: A   79 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7361 (mtt180)
REVERT: A   99 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6777 (p0)
REVERT: A  109 GLN cc_start: 0.7420 (mt0) cc_final: 0.6923 (mp10)
REVERT: A  349 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8529 (mm)
REVERT: B    7 GLN cc_start: 0.7139 (tp40) cc_final: 0.6436 (pt0)
REVERT: B   41 ILE cc_start: 0.8009 (tt) cc_final: 0.7480 (mm)
REVERT: B  104 ARG cc_start: 0.6301 (mmt90) cc_final: 0.5935 (ttm110)
REVERT: B  383 TYR cc_start: 0.8143 (m-80) cc_final: 0.7748 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 86
  average time/residue: 0.0704
  time to fit residues: 8.8737
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0770
   chunk 10 optimal weight:    8.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.140990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.099288 restraints weight = 66271.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.100457 restraints weight = 41115.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.100905 restraints weight = 32982.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.101068 restraints weight = 30752.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.101055 restraints weight = 29517.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6818  Z= 0.127
  Angle     :  0.508   6.853   9238  Z= 0.248
  Chirality :  0.039   0.138    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 13.371 100.534   1135
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.69 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.31), residues: 770
  helix:  2.76 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.23 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.013   0.001   TYR A 169 
 PHE   0.011   0.001   PHE A 275 
 TRP   0.013   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6818)
  covalent geometry    : angle       0.50768 ( 9238)
  hydrogen bonds       : bond        0.04898 (  442)
  hydrogen bonds       : angle       3.82320 ( 1293)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7079 (tp40) cc_final: 0.6386 (tp40)
REVERT: A   79 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7348 (mtt180)
REVERT: A   99 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6770 (p0)
REVERT: A  109 GLN cc_start: 0.7388 (mt0) cc_final: 0.6929 (mp10)
REVERT: A  349 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8513 (mm)
REVERT: B    7 GLN cc_start: 0.7208 (tp40) cc_final: 0.6507 (pt0)
REVERT: B   41 ILE cc_start: 0.8022 (tt) cc_final: 0.7490 (mm)
REVERT: B  104 ARG cc_start: 0.6335 (mmt90) cc_final: 0.5873 (mtm110)
REVERT: B  383 TYR cc_start: 0.8120 (m-80) cc_final: 0.7735 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0675
  time to fit residues: 8.2134
Evaluate side-chains
  84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  246 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0470
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0970
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.3876

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.144204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.102840 restraints weight = 64590.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.104082 restraints weight = 38516.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.104406 restraints weight = 30574.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.104626 restraints weight = 28760.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.104688 restraints weight = 27485.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6818  Z= 0.110
  Angle     :  0.487   6.865   9238  Z= 0.236
  Chirality :  0.038   0.134    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 12.641  94.881   1135
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.42 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.31), residues: 770
  helix:  2.92 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.19 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 105 
 TYR   0.013   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A 275 
 TRP   0.013   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6818)
  covalent geometry    : angle       0.48698 ( 9238)
  hydrogen bonds       : bond        0.04262 (  442)
  hydrogen bonds       : angle       3.74017 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 981.98 seconds
wall clock time: 17 minutes 44.35 seconds (1064.35 seconds total)